RNA interference (RNAi) was originally described as a gene silencing mechanism triggered by the experimental introduction of double stranded (ds)RNA into the nematode C. elegans (Fire et al., 1998). The term RNAi now refers to a diverse set of gene-regulatory mechanisms that share common features, including the involvement of short 21- to 30-nucleotide (nt) RNAs and protein cofactors of the Argonaute (RNase H-related) protein family. As an experimental tool, RN Ai is of broad relevance to basic biomedical research, and RN Ai therapeutics are now approved and under development for several clinical applications. RNAi-related mechanisms function in conserved generegulato1y pathways that are of basic and fundamental importance to human cellular and developmental biology. Remarkably, RNAi-related mechanisms in C.elegans keep inventory of all mRNAs and license gene expression in the germline, passing this information via the egg and sperm from one generation to the next. Distinct Argonaute pathways function in the transgenerational inheritance of small-RNA signals that constitute the CSR-1 self'/protective (RNAa pathway) and the WAGO non-self'/silencing (RNAe pathway). A third Argonaute pathway, the PRG-1/Piwi pathway scans germline mRNA for foreign sequences.
Aim 1 will explore how these Argonaute pathways identify their targets and recruit downstream factors.
Aim 2 will investigate how these Argonaute pathways interact to mediate genome-wide transcriptional surveillance. And finally, Aim 3 will use genetic screens to identify new genes required for RNAi and the related RNAe, RNAa, and newly identified intronless-silencing pathways. The ability to combine classical genetics with technology, including deep-sequencing, facile CRlSPR-mediated genome editing, and proteomics, make C. elegans an ideal system for these studies. The mechanisms and protein families that mediate RNAi are highly conserved in animals and therefore insights from the proposed studies will be directly relevant to human biology and disease. These studies will shed light on an ancient gene-regulatory mechanism whose correlates in humans are likely to play important conserved roles in the protection of the human genome and the maintenance of stem cells.
RNAi-related pathways have deeply conserved connections to chromatin silencing in all Eukarya and play important roles in suppressing transposons in animal genomes. Currently, RNAi is under clinical development for numerous indications, and the first RNAi drug is now approved. The genetic and biochemical studies proposed here will advance our understanding of how RNA-guided mechanisms regulate gene expression, and should also provide insights into both new applications for RNAi in probing gene function and for enhancing the therapeutic potential of RNAi drugs.
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